lncRNA-Chromatin Interaction Analysis

Long non-coding RNAs (lncRNAs) can exert diverse biological functions, including the ability to function as epigenetic modulators and recruit chromatin modifiers to create local chromatin states that allow or block the binding of other regulators. We provide a full range of lncRNA-chromatin interaction analysis services, including RIP-seq, CLIP-seq, eCLIP, ChIRP-seq, and ChIRP-MS, to help you identify lncRNA-chromatin interactions and explore their underlying mechanisms.

Overview

Emerging evidence demonstrates that lncRNAs play a vital role in tissue and developmental-dependent biological functions. Multiple approaches have been developed for global detection of lncRNA-chromatin interactions and probing lncRNA-chromatin structure regulation. Evidence from these approaches identified lncRNAs shown to regulate gene expression through organizing higher order chromatin structure, suggesting that chromatin targeted lncRNAs perform their functions by fine tuning chromatin architecture leading to an altered transcriptional consequence. A few chromatin-associated lncRNAs contain a short common sequence for chromatin targeting. Although thousands of lncRNAs have been identified, some of which can interact with chromatin and recruit proteins to remodel chromatin structure, thus regulating gene expression, how lncRNAs are targeted to chromatin and how lncRNA-chromatin interactions contribute to their biological functions remain largely unknown.

We provide NGS and MS based services for deciphering lncRNA-chromatin interactions, characterizing chromatin-associated lncRNAs, and shedding light on the potential mechanisms by which chromatin-associated lncRNAs exert their functions. Our portfolio for lncRNA-chromatin interaction analysis, including RIP-seq, CLIP-seq, eCLIP, and ChIRP-seq, can generate genome-wide map of lncRNA-chromatin interactions.

Features

Rich ExperienceVarious MethodsValidated ProcessesQuality Control
Rich experience in lncRNA research and bioinformatics analysis.We provide ChIRP-seq, CLIP-seq, RIP-Seq, ChIRP-MS for lncRNA studies. Perform advanced and validated experiments on NGS and MS instruments.Quality control is executed following every procedure.
Data Analysis Workflow

Data Analysis Workflow

In-depth data analysis:

  • Peak calling, motif discovery
  • Identification of lncRNA binding sites
  • Prediction of binding sequence signature(s)
  • Sequence motif analysis
  • GO Term enrichment
  • KEGG pathway analysis
  • Decipher molecular mechanisms

Sample Requirements

(NGS platform) RNA sample (concentration ≥ 200 ng/uL, quantity ≥ 4 ug), 1.8 ≤ OD260/280 ≤ 2.2, OD260/230≥2.0, RIN ≥ 6.5, 28S:18S≥1.0. Please make sure that RNA is not significantly degraded.
(MS platform) We work with a wide range of sample types including protein solution, fresh tissue, cultured cells, blood, and microbial sample. Please feel free to contact us for sample size.

Sample Storage: The sample should be stored at -80°C. Avoid repeated freezing and thawing.

Shipping Method: When shipping the sample, it is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable:

(NGS analysis) FastQ, BAM, coverage summary, QC report, GO enrichment histogram, GO terms DAG (directed acyclic hierarchical graph), and KEGG enrichment scatter plot, and other designated report.
(MS analysis) Data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).

References:

  1. Zhang G, Lan Y, Xie A, et al. Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements. Journal of Biological Chemistry, 2019, 294(43): 15613-15622.
  2. Mishra K, Kanduri C. Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far. Non-Coding RNA, 2019, 5(4): 54.
* For Research Use Only. Not for use in diagnostic procedures.


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